BioC 3.2: CHECK report for CODEX on perceval

Package: CODEX

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CODEX_1.2.0.tar.gz

StartedAt: 2015-11-10 03:33:16 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 03:38:13 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 297.1 seconds

RetCode: 0

Status:  OK

CheckDir: CODEX.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CODEX_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CODEX.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CODEX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CODEX’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CODEX’ can be installed ... [20s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getbambed: no visible global function definition for ‘IRanges’
getcoverage: no visible global function definition for ‘RangesList’
getcoverage: no visible global function definition for ‘IRanges’
getcoverage: no visible global function definition for ‘countOverlaps’
getgc: no visible global function definition for ‘unmasked’
getgc: no visible global function definition for ‘Views’
getgc: no visible global function definition for ‘alphabetFrequency’
getmapp: no visible global function definition for ‘countOverlaps’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [86s/90s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
normalize   36.011  0.807  36.820
normalize2  28.135  0.430  28.566
getcoverage  8.908  0.567  13.201
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/CODEX.Rcheck/00check.log’
for details.

* installing *source* package ‘CODEX’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CODEX)

name	user	system	elapsed
bambedObjDemo	0.001	0.002	0.003
choiceofK	0.012	0.001	0.012
coverageObjDemo	0.001	0.000	0.001
gcDemo	0.002	0.000	0.001
getbambed	0.059	0.002	0.119
getcoverage	8.908	0.567	13.201
getgc	1.109	0.095	1.310
getmapp	0.060	0.006	0.065
mappDemo	0.001	0.000	0.001
mapp_ref	0.007	0.001	0.007
mappability	0.001	0.000	0.001
normObjDemo	0.001	0.000	0.001
normalize	36.011	0.807	36.820
normalize2	28.135	0.430	28.566
qc	0.032	0.000	0.033
qcObjDemo	0.001	0.001	0.001
segment	0.239	0.039	0.278